[English] 日本語
Yorodumi- PDB-7pna: Evolved unspecific peroxygenase with A77L mutation in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pna | ||||||
---|---|---|---|---|---|---|---|
Title | Evolved unspecific peroxygenase with A77L mutation in complex with 12-methoxylauric acid | ||||||
Components | Aromatic peroxygenaseUnspecific peroxygenase | ||||||
Keywords | OXIDOREDUCTASE / 12-methoxylauric acid complex / peroxygenase / peroxidase | ||||||
Function / homology | Function and homology information unspecific peroxygenase / hydrogen peroxide catabolic process / peroxidase activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Agrocybe aegerita (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å | ||||||
Authors | Fernandez-Garcia, A. / Sanz-Aparicio, J. | ||||||
Funding support | Spain, 1items
| ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2023 Title: Engineering a Highly Regioselective Fungal Peroxygenase for the Synthesis of Hydroxy Fatty Acids. Authors: Gomez de Santos, P. / Gonzalez-Benjumea, A. / Fernandez-Garcia, A. / Aranda, C. / Wu, Y. / But, A. / Molina-Espeja, P. / Mate, D.M. / Gonzalez-Perez, D. / Zhang, W. / Kiebist, J. / ...Authors: Gomez de Santos, P. / Gonzalez-Benjumea, A. / Fernandez-Garcia, A. / Aranda, C. / Wu, Y. / But, A. / Molina-Espeja, P. / Mate, D.M. / Gonzalez-Perez, D. / Zhang, W. / Kiebist, J. / Scheibner, K. / Hofrichter, M. / Swiderek, K. / Moliner, V. / Sanz-Aparicio, J. / Hollmann, F. / Gutierrez, A. / Alcalde, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7pna.cif.gz | 85.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7pna.ent.gz | 61.9 KB | Display | PDB format |
PDBx/mmJSON format | 7pna.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/7pna ftp://data.pdbj.org/pub/pdb/validation_reports/pn/7pna | HTTPS FTP |
---|
-Related structure data
Related structure data | 7pn4C 7pn5C 7pn6C 7pn7C 7pn8C 7pn9C 5oxuS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein / Sugars , 2 types, 6 molecules A
#1: Protein | Mass: 35990.012 Da / Num. of mol.: 1 / Mutation: V57A, L67F, V75I, A77L, I248V, F311L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrocybe aegerita (fungus) / Gene: APO1 / Production host: Komagataella phaffii CBS 7435 (fungus) / References: UniProt: B9W4V6, unspecific peroxygenase |
---|---|
#6: Sugar | ChemComp-NAG / |
-Non-polymers , 6 types, 138 molecules
#2: Chemical | ChemComp-PO4 / |
---|---|
#3: Chemical | ChemComp-HEM / |
#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-CL / |
#7: Chemical | ChemComp-7UT / |
#8: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.41 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 1.6M sodium potassium phosphate pH 5.6, 5% MPD Soaking: 40 mM 12-metoxilauric acid, 30 minutes, cryoprotected with 25% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 3, 2020 / Details: KB MIRRORS |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→48.43 Å / Num. obs: 26835 / % possible obs: 99.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.077 / Rrim(I) all: 0.198 / Χ2: 0.94 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 1687 / Rpim(I) all: 0.281 / Rrim(I) all: 0.737 / Χ2: 0.97 / % possible all: 99.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5OXU Resolution: 1.9→48.43 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.691 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.87 Å2 / Biso mean: 17.541 Å2 / Biso min: 8.79 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→48.43 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|